Protein profile

VK055_4737

putative porphyrinogen oxidase

Genome: KpATCC43816

Gene: AIK83271.1 yfeX Structure source: Experimental + ColabFold UniProt A0A0W8ATM9
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Amino acids 299
Annotations 5
Features 9
PDB binders 2
Druggability 0.991

Overview

Basic information about this protein and its source genome.

Accession
VK055_4737
Assembly
Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene
AIK83271.1 yfeX
Status
annotated
Amino acids
299
Structure source
Experimental + ColabFold
EC
1.11.1.-
GO
GO:0020037 Binding to a heme, a compound composed of iron complexed in a porphyrin (tetrapyrrole) ring. GO:0004601 Catalysis of the reaction: a reduced substrate + ROOH = an oxidized substrate + ROH + H2O. GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. GO:0046872 Binding to a metal ion.

Target profile

Computed evidence for target prioritization.

Human off-target
No hit
Human identity (%)
0.0
Gut microbiome off-target
hit
Essential (DEG)
N
DEG identity (%)
28.108
Localization
Cytoplasmic
ColabFold pLDDT
97.53

Selected Druggability evidence

PDB experimental structure

Selected Druggability is the FPocket score chosen for ranking using the curated structure priority. The 3D viewer may show a different loaded structure, so its visible pockets can differ.

FPocket 0.991
Structure 6FIY
Pocket Pocket 1
P2Rank 0.988
Structure 6FIY
Pocket Pocket 1
ColabFold model
FPocket 0.944 · Pocket 1
P2Rank 0.94 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 107 / 4744 genomes with a hit
Normalized 0.023

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 4 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

4
  • GO:0020037 Binding to a heme, a compound composed of iron complexed in a porphyrin (tetrapyrrole) ring.
  • GO:0004601 Catalysis of the reaction: a reduced substrate + ROOH = an oxidized substrate + ROH + H2O.
  • GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
  • GO:0046872 Binding to a metal ion.

Sequence Features

Domain/signature hits from InterPro and related databases.

9 records
Show feature table
Start End DB Term Name
2 298 PANTHER PTHR30521 DEFERROCHELATASE/PEROXIDASE
2 298 InterPro IPR006314 Dyp-type peroxidase
5 294 NCBIfam TIGR01413 Dyp-type peroxidase
5 294 InterPro IPR006314 Dyp-type peroxidase
2 299 ProSiteProfiles PS51404 DyP-type peroxidase family.
2 299 InterPro IPR006314 Dyp-type peroxidase
5 294 Pfam PF04261 Dyp-type peroxidase family
1 297 SUPERFAMILY SSF54909 Dimeric alpha+beta barrel
1 297 InterPro IPR011008 Dimeric alpha-beta barrel

3D Structure

Selected loaded structure. Experimental PDB entries may cover only a portion of the sequence; predicted models typically cover the full protein.

3D visualization script Full viewer

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Structural evidence

12 + 1

Experimental PDB entries and predicted models. Click Switch to display a different structure in the viewer.

Entry Method Resolution Chain Coverage Links Status
PDB 6FIY
X-ray 1.09 Å A,B
100.0% 1-299
PDBe RCSB PDBj File
Viewing
PDB 6FL2
X-ray 1.27 Å A,B
100.0% 1-299
PDBe RCSB PDBj File
Loaded
PDB 6RPD
X-ray 1.52 Å A,B
100.0% 1-299
PDBe RCSB PDBj File
Loaded
PDB 6FKS
X-ray 1.60 Å A,B
100.0% 1-299
PDBe RCSB PDBj File
Loaded
PDB 6RPE
X-ray 1.80 Å A,B
100.0% 1-299
PDBe RCSB PDBj File
Loaded
PDB 6FKT
X-ray 1.86 Å A,B
100.0% 1-299
PDBe RCSB PDBj File
Loaded
PDB 6RQY
X-ray 1.90 Å A,B
100.0% 1-299
PDBe RCSB PDBj File
Loaded
PDB 6RR1
X-ray 1.90 Å A,B
100.0% 1-299
PDBe RCSB PDBj File
Loaded
PDB 6RR4
X-ray 1.90 Å A,B
100.0% 1-299
PDBe RCSB PDBj File
Loaded
PDB 6RR5
X-ray 1.90 Å A,B
100.0% 1-299
PDBe RCSB PDBj File
Loaded
PDB 6RR6
X-ray 1.90 Å A,B
100.0% 1-299
PDBe RCSB PDBj File
Loaded
PDB 6RR8
X-ray 1.90 Å A,B
100.0% 1-299
PDBe RCSB PDBj File
Loaded
ColabFold VK055_4737
ColabFold — — full sequence — Loaded
Pocket details FPocket · P2Rank — toggle visibility and zoom from here, or open full viewer

Pockets (FPOCKET)

Showing top-ranked FPocket candidates by druggability. Druggability is color-coded: high (0.7 or higher), medium (0.4 to 0.69), low (below 0.4).

FPOCKET Sticks Spheres Surfaces Druggability Labels Zoom Positions
2 0.972
1 0.935
26 0.493

Pockets (P2RANK)

Showing top-ranked P2Rank candidates by probability. Probability is color-coded per P2Rank calibration: high (≥ 0.5), medium (0.2 – 0.49), low (< 0.2).

P2RANK Sticks Spheres Surfaces Score Probability Labels Zoom Positions
1 61.75 0.988
2 60.61 0.988
3 32.42 0.943
4 2.88 0.091
5 2.33 0.06

Ligand evidence

Ligands grouped by evidence source. PDB ligands keep the source crystal visible, and loaded crystals can be opened directly in the structure viewer.

2 records

Highest-confidence structural evidence: ligands co-crystallized with this exact protein. If the source PDB is loaded in TPW, use Open crystal to inspect it in the structure viewer.

Show only:
Ligand Source crystal MW · LogP · TPSA Lipinski PAINS SMILES
NO2
6FL2 1.27 Å Open crystal
46.0 Da LogP 0.25 TPSA 52.5 ✓ Ro5 ✓ Clean N(=O)[O-]

PDB and ChEMBL records on this protein are shown in full. ChEMBL records from similar proteins are capped at the top 100 per protein (by pchembl) and ZINC at the top 50 (Tanimoto ≥ 0.5). ADME columns are descriptor-based screening flags, not experimental toxicity results.